Is APOB p.Ile2489Arg (c.7466T>G) pathogenic?

APOB p.Ile2489Arg (c.7466T>G) is classified Uncertain significance in APOB (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-02-10). AlphaMissense: ambiguous (0.3525); Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with APOB p.Ile2489Arg (c.7466T>G)?

APOB p.Ile2489Arg (c.7466T>G) is associated with Cardiovascular phenotype (ClinVar).

How common is APOB p.Ile2489Arg (c.7466T>G) in the general population?

APOB p.Ile2489Arg (c.7466T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about APOB p.Ile2489Arg (c.7466T>G)?

AlphaMissense predicts ambiguous (score 0.3525) — an in-silico prediction, not a clinical call.

APOB p.Ile2489Arg

c.7466T>G · rs2465368781 · VCV1759035

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

ambiguous

0.3525 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.3525	ambiguous
REVEL	0.3	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.9	GERP 1.6, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 9,629 bp · p 0.051 · regional, not allelic
Overall
CADD	23.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: APOB
Protein: p.Ile2489Arg
Coding: c.7466T>G
MANE Select: NM_000384
dbSNP: rs2465368781
Type: single nucleotide variant
Location: chr2:21009402 (GRCh38)
Gene constraint: LOEUF 0.537 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)

Full APOB gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

APOB p.Arg490Trp Pathogenic/Likely pathogenic ★★ same condition
APOB c.1124+3A>G Uncertain significance ★★ same condition
APOB c.11788+4A>G Uncertain significance ★★ same condition
APOB c.12087+2T>C Uncertain significance ★★ same condition
APOB p.Ala1320Thr Uncertain significance ★★ ⚠ same condition
APOB p.Ala1695Val Uncertain significance ★★ ⚠ same condition
APOB p.Ala1975Ser Uncertain significance ★★ ⚠ same condition
APOB p.Ala3008Thr Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/apob-p-ile2489arg (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown